Comparative genomics is a powerful tool for uncovering patterns of mutations within genes targeted for issues in human health. Our research approach utilizes molecular phylogenetic methods and the well-defined evolutionary relationships (based on multiple genetic markers) that unite the 37 species within the cat family Felidae as a reference phylogeny. Current research is focused on the pattern of diversity and substitution in genes located on chromosomes X and Y. Previously, we showed that Y evolve in a highly precise manner and accumulate mutations consistent with the hypothesis of male-driven evolution. Yet we describe an unusual form of recombination exists between X and Y, represented by one-way exon exchange (ectopic gene conversion) from Zfx to Zfy genes. This may be an adaptive mechanism for maintaining function of Y genes located outside the pseudoautosomal region. Ongoing research of sequence diversification in the 4th intron of Smcy in 30 species of Felidae yields new insights on evolution within the NRY demonstrating the phylogenetic importance of insertion/deletions. Moreover, the presence of 2 SINEs in inverse orientation to each other within 2 different unrelated lineages within the cat family provide empirical support for hypotheses concerning possible mechanisms governing SINE insertion, evolution and degradation. We also present links between SINE and microsatellite formation by data describing the evolution and expansion of a microsatellite repeat in the A(T)-rich region of the SINE in cat speciation. Further, we have sequenced Smcy, Zfy and Ube1Y across broader period of evolutionary time represented by the Carnivore order and define a close association between nucleotide substitutions and speciation. Taken together, these data underscore the importance of the Y chromosome in tracking speciation and population history.